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New page: left|200px<br /><applet load="1g3x" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g3x, resolution 2.700Å" /> '''INTERCALATION OF AN...
 
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[[Image:1g3x.gif|left|200px]]<br /><applet load="1g3x" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1g3x, resolution 2.700&Aring;" />
'''INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER'''<br />


==Overview==
==INTERCALATION OF AN 9ACRIDINE-PEPTIDE DRUG IN A DNA DODECAMER==
We present the crystal structure of an acridine drug derivatized at carbon, 9, [N(alpha)-(9-acridinoyl)-tetraarginine], intercalated within the, dodecamer [d(CGCGAATTCGCG)](2). The presence of a lateral chain at the, central carbon 9 atom differentiates this compound from most acridine, drugs hitherto studied, which are usually derivatized at carbon 4. The, DNA:drug interaction we observe differs from that observed in previous, studies, which primarily involves shorter, mainly hexameric sequences, in, two important regards: the acridine intercalates within an AA/TT base, step, rather than within a CG/CG base step; and the binding site is, located at the center of the sequence, rather than at one end of the, duplex. In addition, we observe a novel crystal packing arrangement, with, six dodecamer duplexes and seven hydrated magnesium ions in the asymmetric, unit of a large (66.5 x 68.4 x 77.4 A(3)) unit cell in space group, P2(1)2(1)2(1). The duplexes are organized in layers parallel to the ab, plane, with consecutive layers crossing each other at right angles.
<StructureSection load='1g3x' size='340' side='right'caption='[[1g3x]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1g3x]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3X FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9AC:9-ACRIDINECARBONYL'>9AC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3x OCA], [https://pdbe.org/1g3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3x RCSB], [https://www.ebi.ac.uk/pdbsum/1g3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3x ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We present the crystal structure of an acridine drug derivatized at carbon 9, [N(alpha)-(9-acridinoyl)-tetraarginine], intercalated within the dodecamer [d(CGCGAATTCGCG)](2). The presence of a lateral chain at the central carbon 9 atom differentiates this compound from most acridine drugs hitherto studied, which are usually derivatized at carbon 4. The DNA:drug interaction we observe differs from that observed in previous studies, which primarily involves shorter, mainly hexameric sequences, in two important regards: the acridine intercalates within an AA/TT base step, rather than within a CG/CG base step; and the binding site is located at the center of the sequence, rather than at one end of the duplex. In addition, we observe a novel crystal packing arrangement, with six dodecamer duplexes and seven hydrated magnesium ions in the asymmetric unit of a large (66.5 x 68.4 x 77.4 A(3)) unit cell in space group P2(1)2(1)2(1). The duplexes are organized in layers parallel to the ab plane, with consecutive layers crossing each other at right angles.


==About this Structure==
Intercalation of an acridine-peptide drug in an AA/TT base step in the crystal structure of [d(CGCGAATTCGCG)](2) with six duplexes and seven Mg(2+) ions in the asymmetric unit.,Malinina L, Soler-Lopez M, Aymami J, Subirana JA Biochemistry. 2002 Jul 30;41(30):9341-8. PMID:12135355<ref>PMID:12135355</ref>
1G3X is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G3X OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Intercalation of an acridine-peptide drug in an AA/TT base step in the crystal structure of [d(CGCGAATTCGCG)](2) with six duplexes and seven Mg(2+) ions in the asymmetric unit., Malinina L, Soler-Lopez M, Aymami J, Subirana JA, Biochemistry. 2002 Jul 30;41(30):9341-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12135355 12135355]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1g3x" style="background-color:#fffaf0;"></div>
[[Category: Aymami, J.]]
== References ==
[[Category: Malinina, L.]]
<references/>
[[Category: Soler-Lopez, M.]]
__TOC__
[[Category: Subirana, J.A.]]
</StructureSection>
[[Category: MG]]
[[Category: Large Structures]]
[[Category: dna]]
[[Category: Aymami J]]
[[Category: drug-peptide adduct]]
[[Category: Malinina L]]
[[Category: intercalation]]
[[Category: Soler-Lopez M]]
[[Category: mg+2 ions]]
[[Category: Subirana JA]]
[[Category: x-ray structure]]
 
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